Wonder!

SILAC :: Stable isotope labeling with amino acids in cell culture

2007-01-12T17:02:00.000-05:00

SILAC :: Stable isotope labeling with amino acids in cell culture

Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometric (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given ‘‘light’’ or ‘‘heavy’’ form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, ¹³C, ¹⁵N). Thus in an experiment, two cell populations are grown in culture media that are identical except that one of them contains a ‘light’ and the other a ‘heavy’ form of a particular amino acid (e.g. ¹²C and ¹³C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%.

The site is developed and maintained by Pandey Lab.

HPRD: Human Protein Reference Database

2007-01-04T15:25:00.000-05:00

Human Protein Reference Database (http://www.hprd.org) is a web resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. Information that are cataloged were derived manually by critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.

Cited from http://en.wikipedia.org/wiki/HPRD

Tree of Life Web Project

2006-12-20T18:06:00.000-05:00

Tree of Life Web Project is a collaborative effort of biologists from around the world. On more than 5000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics.

Each page contains information about a particular group of organisms (e.g., echinoderms, tyrannosaurs, phlox flowers, cephalopods, club fungi, or the salamanderfish of Western Australia). ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.

A chapter on Patterson Function

2006-12-12T18:06:00.000-05:00

The Patterson Function

Eclipse Plug-In for R: "StatET"

2006-12-08T18:12:00.000-05:00

"StatET" is a small Eclipse plug-in, supporting you to write R scripts and documentations.

R is "a language and environment for statistical computing and graphics". Eclipse is "a kind of universal tool platform - an open extensible IDE for anything and nothing in particular". Both are available for many operation systems and can be used for free, and -of course- this plug-in too.

Population Education

2006-11-13T16:15:00.000-05:00

Population Education:

Get a Free USA at 300 Million Wall Chart

"2006 marks an historic milestone for our nation -- 300 million people. Over the past century, the population has tripled, making the United States the fastest growing developed country in the world, and the third largest overall. Reaching this marker offers an opportunity to reflect on our past, examine current trends and articulate our hopes for the future of American society."

The Jax Lab - Mice Genetics

2006-11-07T17:33:00.000-05:00

The Jackson Laboratory- Advancing Research in Human Health

They maintain over 3 ooo mouse strains, which are widely used around the world. Their website also hold a lot of FREE research resources on mouse genetics. Check it out at http://www.jax.org/

Answers.com - Online Dictionary, Encyclopedia and much more

2006-11-04T15:43:00.000-05:00

Answers.com - Online Dictionary, Encyclopedia and much more:

Embryo Images Online

2006-11-03T13:21:00.000-05:00

Embryo Images Online: Normal & Abnormal Mammalian Development

Olympus Microscopy Resource Center

2006-11-01T12:08:00.000-05:00

Olympus Microscopy Resource Center is designed to provide an Internet-based educational forum on all aspects of optical microscopy, photomicrography, and digital imaging. Many renowned manuals and interactive tutorials are avaible for FREE.
Also see Introduction to Optical Microscopy, Digital Imaging, and Photomicrography.

The WWW Virtual Library

2006-10-21T13:19:00.000-04:00

The WWW Virtual Library is the oldest catalogue of the Web, started by Tim Berners-Lee, the creator of HTML and of the Web itself, in 1991 at CERN in Geneva. Unlike commercial catalogues, it is run by a loose confederation of volunteers, who compile pages of key links for particular areas in which they are expert; even though it isn't the biggest index of the Web, the VL pages are widely recognised as being amongst the highest-quality guides to particular sections of the Web.

Agriculture
Irrigation, Livestock, Poultry Science, …
The Arts
Art History, Classical Music, Theatre and Drama, …
Business and Economics
Finance, Marketing, Transportation, …
Communications and Media
Broadcasters, Publishers, Telecommunications, …
Computing and Computer Science
Artificial Intelligence, Cryptography, Logic Programming, …
Education
Primary, Secondary, Tertiary, …
Engineering
Architecture, Electrical, Mechanical, …
Humanities and Humanistic Studies
History, Languages and Linguistics, Museums, …

Information and Libraries
Information Quality, Knowledge Management, Libraries, …
International Affairs
International Relations and Security, Sustainable Development, …
Law
Arbitration, Forensic Toxicology, Legal History, …
Natural Sciences and Mathematics
Biosciences, Earth Science, Medicine and Health, Physics, …
Recreation
Gardening, Recreation and Games, Sport, …
Regional Studies
African, Asian, Latin American, European, …
Social and Behavioural Sciences
Anthropology, Archaeology, Population and Development Studies, …
Society
Peoples, Religion, Gender Studies, …

The World-Wide Web Virtual Library: Statistics

2006-10-17T21:03:00.000-04:00

The World-Wide Web Virtual Library: Statistics

The World Wide Web Virtual Library: Statistics

This page is being brought to you by the folks at The University of Florida's Department of Statistics.
The "book and globe" logo is the trademark of the WWW Virtual Library.

Data Sources

Statistical Reference Datasets (StRD)

Job Announcements

The Job Announcements are maintained at UF. Announcements may be sent via email to jobs@stat.ufl.edu .

Departments, Divisions, and Schools of Statistics

Listings by Continent: [Africa] [Asia] [Australia/Oceania] [Europe] [North America] [South America]

On-Line Educational Resources

Government Statistical Institutes

Statistical Research Groups, Institutes, and Associations

Statistical Services

Advanced Quantitative Services
BS Statistics
Business Statistics (Graduate)
Stat-Ease
Stat Guide Online
Statistical Data Analysis (Undergraduate)
Systems Simulation (Graduate)
Venturi Technology Partners

Statistical Archives and Resources

A Bare Bones Introductory Statistics Text Book
Bibliography for Computational Probability and Statistics
Bibliography for Discrete Event Simulation
Bibliography for Optimization with Sensitivity Analysis
CHANCE Database
CSIRO QStats Software a directory of statistical software sites
David Dowe's Mixture Modelling Page
Fortran 90 Web Site of Alan J. Miller -- Fortran code for statistics
Free Statistical Tools on the Web
JASA Data Archive
GAMS: Guide to Available Mathematical Software
Introductory Statistics: Concepts, Models, and Applications
Macintosh-based statistics software
Math Jobs -- Listing of Jobs Related to Mathematics
Netlib (Mathematical and Statistical Software)
Probability/Statistics Object Library
PASE
Quick-Start Guide to Common Calculators
Manuscript Collections in the Statistical Archive, Iowa State University Library
Service Industries Trends (SItrends.org)
StatLib Index
Statistics HomePage -- Electonic Statistics Texbook
Statistics on the Web
StatsNet
stats.repsys.net
SunSITE, Austria -- Computer Support for Mathematics, Statistics & Science Education
Tutorials: Statistics
U.S. Bureau of Labor Statistics
U.S. Census Bureau

Statistical Software Vendors and Software FAQs

Accumetric Corporation -- AccuCon, AccuROC
Analyse-It Software Ltd. -- Analyse-It for Microsoft Excel
Analytical Software -- Statistix
Aptech Systems -- GAUSS
Automatic Forecasting Systems -- AUTOBOX
Circle Systems -- Stat/Transfer
Click and Learn Regression
CoHort Software -- Graphics and Statistics Software for Scientists and Engineers
Creascience -- XLSTAT
CyTEL Software Corporation -- StatXact, LogXact, EaSt
Data Description, Inc. -- Data Desk, Viz!on, ActivStats
Data Step -- Free SPSS tutorial and statistical selection guide
Data Shaping Solutions
DOS-based statistics software
DTREG -- Generates classification and regression decision trees.
ESB Consultancy -- ESBStats, ESBPDF, ESBCalc
Exeter Software -- NTSYSpc
Expert Health Data Programming -- Vitalnet
GRABITECH
GraphPad Software -- Prism, InStat
High Performance Systems -- ithink, STELLA
InterLeap
John Galt Solutions -- ForecastX
Kovach Computing Services -- xlSTAT, MVSP
Leading Market Technologies -- EXPO
Lumina Decision Systems -- Analytica
Macsyma Inc. -- Macsyma, PDEase2D
Manugistics, Inc. -- STATGRAPHICS
Mathsoft, Inc. -- Mathcad and S-PLUS
MATHSTATICA Pty Ltd - mathStatica
Mathtools.com -- Complementary products for MATLAB
Mathtools.net -- Portal for MATLAB
MathWorks -- MATLAB
MedCalc
MicroMetrix -- AssiStat
Mike McLaughlin -- Regress+ for MacOS
Minitab, Inc.
MultiSimplex
NCSS
NLREG -- Performs general nonlinear regression.
Numerical Algorithms Group -- Genstat, GLIM, NAG Libraries
OriginLab -- Origin
Partek Pro Software
POSDEM -- Software to choose between sampling plans
Process Builder -- STRATEGY
ProGAMMA -- Software for the Social and Behavioral Sciences
Provalis Research -- SIMSTAT
QQQ Software -- TPL Tables
Qualitran's Statistical Software
Resampling Stats
Raynald's SPSS Tools, Archive, Tips, FAQ and Tutorials
Salford Systems - Statistical Software and Consulting
The SAS Institute
Obtaining SAS Notes through Email
Scolari Sage Publications -- GB STAT
Seventh Sense Software -- Chameleon Statistics
S-Matrix Corporation -- CARD - Design Of Experiments software for Windows
SPSS
Scientific Software International -- LISREL & HLM
The S FAQ
SmallWaters Corp.Amos structural equation modeling
Stata Corporation
Stat-Ease
Statistical Solutions -- SOLAS for Missing Data Analysis
Statpoint.com -- STATGRAPHICS Plus, STATLETS, STATBEANS
StatSoft, Inc. -- STATISTICA
StatsDirect
Statit Software -- Statit e-QC, Statit e-Server, Statit Custom QC
StudySize
SUDAAN
Visual Numerics Inc. -- PV-Wave, IMSL, Stanford Graphics.
Wolfram Research -- Mathematica
xlSTAT HomePage
XLStatistics
XploRe -- Interactive Statistical Computing Environment
XTREMES

Statistical Journals

Mailing Lists and Archives

AI-Geostats, a Geostatistics mailing list
Allstat
Allstat Web Intro
Genstat (searchable archive)
List of Statistics Lists
S-news
SAS-L (WAIS Archive)
SPSS-L (WAIS Archive)

Statistics Related News Groups

Related Fields

From: http://www.stat.ufl.edu/vlib/

3DGenome Project

2006-10-05T22:33:00.000-04:00

3DGenome Project consortium members will develop state-of-the-art 3D light microscopy techniques, along with image processing and analysis tools to visualise DNA inside the cell. They will correlate the genome's 3D structure with the expression of specific genes in human, mice and drosophila cells. Using this range of model systems will help establish which aspects of the 3D genome structure have been conserved through evolution and which are most likely to play an important role in gene regulation.

The research program is conducted by a consortium of seven European partners and is coordinated by Roel van Driel of the Swammerdam Institute for Life Sciences of the University of Amsterdam in The Netherlands.

The EU Sixth Framework Programme (FP6) for Research and Development (2002-2006) is one of the world's largest research programmes, with a budget of 17.5 billion Euros, of which around 3 billion Euros is available for life sciences research. Under the FP6, 2.2 million Euros have been awarded to the 3DGENOME-research program.

Molecular Probes - The Handbook - A Guide to Fluorescent Probes and Labeling Technologies(10th)

2006-10-05T15:49:00.000-04:00

The Handbook — A Guide to Fluorescent Probes and Labeling Technologies is a comprehensive resource for fluorescence technology and its applications. Newly revised, The Handbook contains detailed information describing the use of more than 3000 Molecular Probes products for life science research, including extensive data, numerous technical notes, and full-color images of the products in action.

Introduction to Fluorescence Techniques

Chapter 1
Fluorophores and Their Amine-Reactive Derivatives

Chapter 2
Thiol-Reactive Probes

Chapter 3
Reagents for Modifying Groups Other Than Thiols or Amines

Chapter 4
Biotin Derivatives and Haptens

Chapter 5
Crosslinking and Photoactivatable Reagents

Chapter 6
Ultrasensitive Detection Technology

Chapter 7
Antibodies, Avidins, Lectins and Related Products

Chapter 8
Nucleic Acid Detection and Genomics Technology

Chapter 9
Protein Detection and Proteomics Technology

Chapter 10
Enzyme Substrates

Chapter 11
Probes for Cytoskeletal Proteins

Chapter 12
Probes for Organelles

Chapter 13
Probes for Lipids and Membranes

-

Chapter 14
Fluorescent Tracers of Cell Morphology and Fluid Flow

Chapter 15
Assays for Cell Viability, Proliferation and Function

Chapter 16
Probes for Endocytosis, Receptors and Ion Channels

Chapter 17
Probes for Signal Transduction

Chapter 18
Probes for Reactive Oxygen Species, Including Nitric Oxide

Chapter 19
Indicators for Ca{2+}, Mg{2+}, Zn{2+} and Other Metal Ions

Chapter 20
pH Indicators

Chapter 21
Indicators for Na{+}, K{+}, Cl{-} and Miscellaneous Ions

Chapter 22
Probes for Membrane Potential

Chapter 23
Tools for Fluorescence Applications, Including Reference Standards and Optical Filters

Technical Notes and Product Highlights

List of Tables

List of Figures

Provided by

GeneScape Portal

2006-10-05T10:46:00.000-04:00

GeneScape® is CuraGen's state-of-the-art operating portal that provides the foundation for genomic-based drug discovery and development. GeneScape is a sophisticated bioinformatics platform that was developed at CuraGen to manage, track, analyze, and interpret industrial scale genomic information. The GeneScape operating portal integrates each of CuraGen's functional genomic technologies and enables access via the Internet.

Gene Ontology Tools

2006-10-02T00:19:00.000-04:00

Gene Ontology Tools

Tools for searching and browsing GO

Annotation tools

Tools for gene expression/microarray analysis

Other tools

Consortium Tools

The tools below are developed within the Gene Ontology Consortium. They continue to be improved and expanded and you can receive support in using these tools by writing to the GO helpdesk.

The tools on this page are free to academics.

AmiGO

Berkeley Bioinformatics and Ontology Project
No abstract available

AmiGO allows you to search for a GO term and view all gene products annotated to it, or search for a gene product and view all its associations. You can also browse the ontologies to view relationships between terms as well as the number of gene products annotated to a given term. AmiGO accesses the GO mySQL database; the browser and documentation are available from the GO database website.

AmiGO is developed and maintained within the GO Consortium.

OBO-Edit

Berkeley Bioinformatics and Ontology Project
No abstract available

OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies.
OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.
OBO-Edit was previously known as DAG-Edit.
OBO-Edit uses the OBO format flat file.
OBO-Edit is developed and maintained within the GO Consortium.

Non-Consortium Tools

Many tools have been created outside of the consortium for use with the GO ontologies. To see listings of these tools please use the links in the table below.

Tools for searching and browsing GO

Tool to display, browse and search the ontologies and/or annotations.

Annotation tools

Tools for annotating genes or gene products using GO

Tools for gene expression/microarray analysis

Other tools

Submit new tools

How to request that your tool be listed on these pages.

From: http://www.geneontology.org/GO.tools.shtml

Data Analysis BriefBook

2006-09-25T15:56:00.000-04:00

The Data Analysis BriefBook is a condensed handbook, or an extended glossary, written in encyclopedic format, covering subjects in statistics, computing, analysis, and related fields. It intends to be both introduction and reference for data analysts, scientists and engineers.

Moved to Wonder! China

2006-06-26T17:20:00.000-04:00

Friends in China can not visit Blogger, so I finally decide to move to Wonder！- Learning .:&:. Amusement (http://sparkw.mysmth.net/) or visit by another address given by China's SciBlogger Association (http://biowonder.sciblogs.org）

Please visit my home page http://jieqi.info for other sharing.

Gene Ontology

2006-06-15T23:19:00.000-04:00

Gene Ontology(GO) project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. The three organizing principles of GO are molecular function, biological process and cellular component.

General Repository for Interaction Datasets

2006-06-15T23:16:00.000-04:00

General Repository for Interaction Datasets (GRID) is a comprehensive database of Genetic and Physical Interactions in several organisms, including yeast, fly and worm. They also develop a software named Osprey to view those interactions locally. Osprey builds data-rich graphical representations from Gene Ontology(GO) annotated interaction data maintained by The GRID.

Directory of Grants and Fellowships in the Global Health Sciences

2006-06-15T13:13:00.000-04:00

The Fogarty International Center, the international component of the National Institutes of Health, addresses global health issues through research and training programs and participates in international partnerships to foster research and improve health. Since 1988, the Center has published the Directory of International Grants and Fellowships in the Health Sciences, a comprehensive compilation of international funding opportunities in biomedical and behavioral research. RSS Feed.

Phobius

2006-06-15T13:10:00.000-04:00

Phobius: "A combined transmembrane topology and signal peptide predictor"

Eukaryotic Promoter Database (SIB)

2006-06-15T02:05:00.000-04:00

SIB-EPD is an annotated non-redundant collection of eukaryotic POL II promoters. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Powered by Swiss Institute for Bioinformatics

Saccharomyces Genome Database

2006-06-14T12:41:00.000-04:00

SGD^TM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

Bioinformatics: Sequence and Genome Analysis (2nd Edt)

2006-06-14T02:02:00.000-04:00

Read it Online
The second edition of Bioinformatics: Sequence and Genome Analysis provides comprehensive instruction in computational methods for analyzing DNA, RNA, and protein data, with explanations of the underlying algorithms, the advantages and limitations of each method, and strategies for their application to biological problems.